Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica

Genome Biology
Cizhong JiangThomas Peterson

Abstract

Myb proteins contain a conserved DNA-binding domain composed of one to four repeat motifs (referred to as R0R1R2R3); each repeat is approximately 50 amino acids in length, with regularly spaced tryptophan residues. Although the Myb proteins comprise one of the largest families of transcription factors in plants, little is known about the functions of most Myb genes. Here we use computational techniques to classify Myb genes on the basis of sequence similarity and gene structure, and to identify possible functional relationships among subgroups of Myb genes from Arabidopsis and rice (Oryza sativa L. ssp. indica). This study analyzed 130 Myb genes from Arabidopsis and 85 from rice. The collected Myb proteins were clustered into subgroups based on sequence similarity and phylogeny. Interestingly, the exon-intron structure differed between subgroups, but was conserved in the same subgroup. Moreover, the Myb domains contained a significant excess of phase 1 and 2 introns, as well as an excess of nonsymmetric exons. Conserved motifs were detected in carboxy-terminal coding regions of Myb genes within subgroups. In contrast, no common regulatory motifs were identified in the noncoding regions. Additionally, some Myb genes with similar...Continue Reading

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Citations

May 14, 2011·The Journal of Heredity·Ryoji TakahashiSetsuko Komatsu
Oct 3, 2006·Plant Physiology·Adam M TakosAmanda R Walker
Dec 19, 2008·Plant Physiology·Olivia WilkinsMalcolm M Campbell
Oct 11, 2005·The Plant Cell·Ryushiro D KasaharaGary N Drews
Jul 11, 2012·BMC Plant Biology·Hai DuYi-Xiong Tang
Jun 22, 2012·PloS One·Hai DuYi-Xiong Tang
Dec 29, 2012·International Journal of Molecular Sciences·Wenjun HuangYing Wang
Jul 21, 2011·Journal of Nucleic Acids·Lilian Cristina Baldon Aizza, Marcelo Carnier Dornelas
Jan 24, 2014·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Feng WenZhaoqing Chu
Feb 2, 2016·International Journal of Molecular Sciences·Yahui HanHaiyang Jiang
Feb 8, 2006·Biochemical and Biophysical Research Communications·Jigang LiHongya Gu
Jul 10, 2014·Molecular Genetics and Genomics : MGG·Panpan ZhaoZhonghai Ren

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Datasets Mentioned

BETA
BAC79618
AF466202

Software Mentioned

YN00
PlotSimilarity GCG
MEGA
HMMER
Blastp search
PAML
FGeneSH
BLAST
GenScan
MEME

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